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If you have a site that has been matched with a brand then Google will rarely remove your site entirely from the index. Take JC Penny for example. They didn't suffer any rankings for the term JC Penny. They suffered rankings for other terms that they had been building bad links for. Monitoring your keyword rankings and noticing large drops in positions on a per keyword base might give you a better idea if you have been hit with a penalty.

Verify your site in Google Webmaster Tools, and see if there is a notice from Google there. They will sometimes notify you if you have a penalty. If you are completely out of the index, you can file a reinclusion request in GWT as well.

If you want to put your URL here, the community can take a look and see what they can find that may help answer your question, if it is not purely a hypothetical question.

Do a search for site:mydomain.com in Google. If nothing comes up, you have been given the stiffest penalty out there, complete removal from the index.

Try a google search for just your brand name. Are you in the top ten? If not, you are probably being penalized.

Go to your Google analytics. Look at traffic sources and just go to the Google data. Has there been a steep decline somewhere in traffic from Google? You probably have a penalty.

Look at your website content. Do you have hidden text the same color as the background? Do you link out to spammy viagra and gambling sites? Do you have more than 500 links on one page? Is your site keyword gibberish that doesn't even make grammatical sense? Is your keyword bolded every time? Then if you don't yet have a penalty, you probably will soon.

Look at your backlinks to your website. Have you paid for any of those links? Do you exclusively have reciprocal links? Do all your links come from spammy sites? Do all your links have identical anchor text? Do all your links only go to your homepage? Do all your links come from the same c-block? Then if you don't yet have a penalty, your probably will soon.

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